X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KAL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.151.4 M D-malic acid with the addition of 2.5 mM y-EC, 2.5 mM ADP, 5 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
3.1460.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.39α = 90
b = 154.39β = 90
c = 344.325γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.98DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.485099.80.1450.154128.9143724
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.541.2381.309

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3KAL2.4850140946724099.960.22490.22410.2414RANDOM49.843
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
2.52.5-4.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.652
r_dihedral_angle_4_deg17.107
r_dihedral_angle_3_deg14.588
r_dihedral_angle_1_deg6.031
r_angle_refined_deg1.389
r_angle_other_deg0.922
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.652
r_dihedral_angle_4_deg17.107
r_dihedral_angle_3_deg14.588
r_dihedral_angle_1_deg6.031
r_angle_refined_deg1.389
r_angle_other_deg0.922
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21465
Nucleic Acid Atoms
Solvent Atoms401
Heterogen Atoms268

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data processing
MOLREPphasing